In utero exposure to environmental chemicals or drugs accounts for approximately 5% of all birth defects and can have an impact in adult life by disrupting the epigenetic developmental programs that are activated later in life (e.g., puberty, aging). The currently accepted regulatory test for identifying potential teratogens involves the use of thousands of animals, is costly, takes two years to complete, and shows poor concordance (~60%) for human teratogens. The recent European Union ban on animal testing makes the reliance on non-animal test systems more urgent. Human embryonic stem (hES) cells reflect a unique biological system that cannot be represented by any other cell type used in toxicology. This proposal is focused on developing and validating a rapid toxicogenomics-based signature profiling assay for seamless integration into the Stemina Biomarker Discovery devTOX(tm) metabolomics-based platform. The combined expertise at ILS and Stemina will enable an innovative systems biology approach to in vitro developmental toxicology screening in a human-relevant assay using the cell type at the origin of human development, the hES cell. We will identify a toxicogenomics-based signature profile built on the unique stem cell transcriptome response (protein coding mRNA and non-coding RNAs), and cellular response pathways to toxicant exposures, using bioinformatics-driven computational methods. Ultimately, this Phase II SBIR will result in the development, validation, and implementation of a medium throughput assay using transcriptome-based profiling with a high predictive value for potential developmental toxicants. This objective will be completed in three Specific Aims: Specific Aim 1: Conduct expression profiling of hES cells exposed to known/suspect teratogens and nonteratogens using a training set of 62 compounds to construct a predictive transcriptome-based signature of developmental toxicity; Specific Aim 2: Develop and implement bioassay standard operating procedures, quality control criteria, and validation of instrumentation and GLP-compliant protocols for the conduct of the devTOX(tm) assay integrated with transcriptomics; Specific Aim 3: Test the transcriptome-based signature derived from the training set with a blinded set of test articles using qRT-PCR assays for specific mRNAs, lncRNAs and miRNAs. This will allow development of a biologically relevant signature profile based on dysfunction of the highly regulated genome and epigenome circuitry that maintains stem cell functions.